UNIT 3.7 An Overview of Multiple Sequence Alignment

  1. Victor Simossis,
  2. Jens Kleinjung,
  3. Jaap Heringa

Published Online: 1 NOV 2003

DOI: 10.1002/0471250953.bi0307s03

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Simossis, V., Kleinjung, J. and Heringa, J. 2003. An Overview of Multiple Sequence Alignment. Current Protocols in Bioinformatics. 3:3.7:3.7.1–3.7.26.

Author Information

  1. Integrative Bioinformatics Institute (IBIVU), Free University, Amsterdam, The Netherlands

Publication History

  1. Published Online: 1 NOV 2003
  2. Published Print: SEP 2003


Multiple sequence alignment is perhaps the most commonly applied bioinformatics technique. It often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families. In this unit, an overview of multiple sequence alignment techniques is presented, covering a history of nearly 30 years from the early pioneering methods to the current state-of-the-art techniques. Methodological and biological issues and end-user considerations, as well as alignment evaluation issues, are discussed.